Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis)

Feng, Shuo; Li, W. G.; Huang, Hong; Wang, J. Y.; Wu, Yan

doi:10.1007/s11032-008-9216-0

Cited by 157 publications

(168 citation statements)

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“…The gSSR 268 primer pairs generated the highest number allele per locus (N), polymorphic information content (PIC), observed heterozygosity (Ho) and expected heterozygosity (He) while HBE 280 primers generated the lowest for most of the genetic parameters (Table 2). The average number of allele per locus, PIC, Ho and He obtained in this study were higher than those in previously reported results (Feng, Li, Huang, Wang, & Wu, 2009;Triwitayakorn et al, 2011;Perseguini et al, 2012). The differences may be due to the type and the number of populations analyzed in this study from the previous ones.…”

Section: Allelic and Population Genetic Diversitycontrasting

confidence: 88%

“…Although the EST-SSR markers tend to be less polymorphic than the genomic SSR, EST-SSR is better in their ability to differentiate accessions belonging to closely related species (Feng, Li, Huang, Wang, & Wu, 2009). Many research groups have developed the EST-SSR for rubber trees (Ko, Chow, & Han, 2003;Chow et al, 2007;An, Zhao, Cheng, Li, & Huang, 2009;Triwitayakorn et al, 2011;Xia et al, 2011;Li, Deng, Qin, Liu, & Men, 2012;Mantello, Suzuki, Souza, Gonçalves, & Souza, 2012;An et al, 2013;Cubry et al, 2014;Li, Deng, Guo, Xia, 2014;Silva et al, 2014).…”

Section: Introductionmentioning

confidence: 99%

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Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

et al. 2017

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The accession of the IRDB 1981 (PN'81) population is a newly introduced and an important rubber tree germplasm while the Wickham clone is a commercial variety one. The objectives of this study were to assess the genetic diversity and the population structure of PN'81 populations and the Wickham clones using 15 EST-SSR loci. Results of the analysis showed that the evaluated SSR primers yielded polymorphic markers. The gSSR 268 primer pairs yielded the most informative markers while HBE 280 primers generated the lowest ones. Results of the genetic diversity analysis supported that the PN'81 population belonged to a single large natural population of rubber trees while the Wickham clones belonged to a different group than that of PN'81. The population structure analysis of the rubber accessions was also in agreement with the results of the genetic diversity analysis. The experiment also indicated that PN'81 populations would be useful for future rubber breeding in Indonesia, especially as the sources of parent clones for rubber tree hybridization programs and rubber tree genetic resource conservation.

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Section: Allelic and Population Genetic Diversitycontrasting

confidence: 88%

Section: Introductionmentioning

confidence: 99%

Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

et al. 2017

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“…In earlier reports, di, tri and tetra motif loci polymorphism proportion amounted to 54.8, 28.8 and 47 % whereas TTNRs and PNRs were randomly distributed (Sharma and Chauhan 2011). Higher order repeat motifs (more than three bases) as well as the compound repeat were found to have less polymorphism as compared to lower order repeats (Feng et al 2009). Such amplification and polymorphism represented primers which contained more than 15 repeat units (Sharma and Chauhan 2011).…”

Section: Genetic Diversitymentioning

confidence: 72%

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Thatikunta¹,

Sankar²,

Sreelakshmi³

et al. 2016

Physiol Mol Biol Plants

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Castor (Ricinus communis L.) a chief non-edible oilseed crop has numerous industrial applications. Systematic genetic diversity analysis utilizing DNA based markers has been quick and reliable method that ensures selection of diverse parents for exploitation of higher levels of heterosis in breeding programs. From NCBI database, 63,852 EST sequences of castor were mined. One thousand one hundred and five (1105) EST-SSRs and 1652 repeat motifs sequences were identified from 20,495 non-redundant unigene sequences. Repeat motifs consisted of 29.7 % mono nucleotide repeats, 24.8 % di nucleotide repeats, 27.27 % tri nucleotide repeats and 3.94 % tetra nucleotide repeats. Twenty eight primer pairs were chosen from SSRcontaining ESTs to determine genetic diversity among 27 castor accessions. Twelve EST-SSRs showed polymorphism. Number of alleles detected were 2-3 with an average of 2.33 per locus. 150-400 bp was the size of an allele. Dendrogram analysis grouped the 27 accessions into two separate clusters. Genetic similarity coefficient of dendrogram ranged from 0.24 to 0.83. The polymorphic information content value of 0.28-0.49 revealed medium level of diversity in castor. Results of present study indicated that EST-SSRs to be efficient markers for genetic diversity studies. Knowledge on level of diversity existing in castor genotypes would be useful for breeders to plan efficient hybrid breeding programme.

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“…EST-derived SSRs have been well documented in some plant species including Arabidopsis (Depeiges et al, 1995), sugarcane (Cordeiro et al, 2001), cereal species (Kantety et al, 2002), cacao (Lima et al, 2008), and rubber tree (Feng et al, 2009). Recently, many EST libraries of a wide range of plant species have been constructed for genes involved in plant growth and differentiation (Matsuoka et al, 2004), biochemical pathways (Remy and Michnick, 2004;Urbanczyk-Wochniak and Sumner, 2007), secondary metabolism (Park et al, 2004), and responses to environmental stresses and pathogen attack (Sugui and Deising, 2002).…”

Section: Introductionmentioning

confidence: 99%

Characterization of EST-derived and non-EST simple sequence repeats in an F1 hybrid population of Vitis vinifera L.

Kayesh¹,

Bilkish²,

Liu³

et al. 2014

Genet. Mol. Res.

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ABSTRACT. Among different classes of molecular markers, expressed sequence tags (ESTs) are a new resource for developing simple sequence repeat (SSR) functional markers for genotyping and genetic mapping in F 1 hybrid populations of Vitis vinifera L. Recently, because of the availability of an enormous amount of data for ESTs in the public domain, the emphasis has shifted from genomic SSRs to EST-SSRs, which belong to transcribed regions of the genome and may have a role in gene expression or function. The objective of this study was to assess the polymorphisms among 94 F 1 hybrids from "Early Rose" and "Red Globe" using 25 EST-derived and 25 non-EST SSR markers. A total collection of 362,375 grape ESTs that were retrieved from the National Center for Biotechnology Information (NCBI) and 2522 EST-SSR sequences were identified. From them, 205 primer pairs were randomly selected, including 176 pairs that were EST-derived and 29 non-EST SSR primer pairs, for polymerase chain reaction amplification. A total Characterization of EST and non-EST SSRs in grapevine of 131 alleles were amplified using 50 pairs of primers; 78 alleles were amplified using EST-derived SSR primers and 53 were from non-EST SSR primers. At most, 6 and 5 alleles were amplified by EST-derived and non-EST SSR primers, respectively. The EST-derived SSR markers showed a maximum polymorphic information content (PIC) value of 1 and a minimum of 0.33 while non-EST SSR markers had maximum and minimum PIC values of 1 and 0.25, respectively. The average PIC value was 0.56 for EST-derived SSR markers and 0.45 for non-EST SSR markers.

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Development, characterization and cross-species/genera transferability of EST-SSR markers for rubber tree (Hevea brasiliensis)

Cited by 157 publications

References 50 publications

Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

Genetic Diversity and Population Structure of IRRDB 1981 and Wickham Rubber Germplasm Based on EST-SSR

Utilization of in silico EST–SSR markers for diversity studies in castor (Ricinus communis L.)

Characterization of EST-derived and non-EST simple sequence repeats in an F1 hybrid population of Vitis vinifera L.

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